Creatig and using an OTU reference file

I am limited by the number of samples I can run with MOTHUR.
I am trying to create a reference file so that the OTU’s match up between each after runing them through the MiSeq SOP.
I have read through the classify.otu command and am unsure how to go about this.


I’m pretty sure this won’t work. OTUs are data dependent and have to be updated as more data are added. Why are the number of samples you can run limited? Usually this is a sign that people aren’t using the right region or chemistry:

Thanks Pat

That link was very informative.

The Idea I had was using the OTU list from the first set of samples run through Mothur, to match up any common OTU’s in the second set of data.
That way the OTU’s would be labeled the same, allowing analysis between the two sample sets (these samples were sequenced on the same plate).
I thought this could be done through the classify.otus command.